The isolation of unknown compounds for structural identification and the collection of target molecules to generate unavailable standards remain a challenge when dealing with complex sample. While tedious multistep purification is commonly used, it is not appropriate for a limited amount of sample or when a full recovery of expensive molecules is required. Two-dimensional preparative chromatography in a comprehensive mode provides an effective mean to collect a large number of molecules in such a case. However, there is currently a lack of metrics to estimate preparative performances with a minimal number of experiments. An in silico comparative study of various pairs of chromatographic systems is proposed, focusing on the occupation rate and the homogeneity of peak spreading in the 2D separation space. Off-line combination of centrifugal partition chromatography (CPC) with liquid chromatography (LC) exhibits numerous advantages for 2D preparative separation. Our in silico approach was illustrated through the isolation of eight bioactives compounds with very similar structures from Cyclopia genistoides plant by CPCxLC. The column screening was performed considering predictive 2D plots in the light of the preparative performance descriptors and compared to real 2D preparative separations.